Mortality in Europe

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Question

What is the annual mortality rate in Europe per country and ICD10 category?

Indices

Country (Geo)
Cause of death (Icd10)
Age
Sex
Year
Unit of measurement (Unit) RT means standardised mortality rate.

Answer

Example graphs from the data. [1]

+ Show code - Hide code

library(OpasnetUtils)
library(ggplot2)

d <- opbase.data("Op_en4635", subset = "d", include = list(Icd10 = c("W65-W74", "X60-X84_Y870", "X85-Y09_Y871")))
d$Year <- as.factor(d$Year)
d$Result <- as.numeric(as.character(d$Result))

ggplot(subset(d, Icd10 == "W65-W74"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Drowning per 100000 py")
ggplot(subset(d, Icd10 == "X60-X84_Y870"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Self-harm per 100000 py")
ggplot(subset(d, Icd10 == "X85-Y09_Y871"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Assault per 100000 py")

Rationale

Data

The main data comes from Eurostat from where the file "Causes of death - standardised death rate per 100 000 inhabitants - annual Data (hlth_cd_asdr)" was downloaded on 12th Jan 2015 and stored in Opasnet base.

Other data:

WHO Mortality Database

Unit

Standardised incidence (1/100000py)
Deaths/year

Calculations

This code was used to manage the data before using the OpasnetBaseImport.

Show details

library(reshape2)
library(OpasnetUtils)

d <- read.table("//cesium/jtue$/_Downloads/hlth_cd_asdr.tsv", sep = "\t")
d1 <- strsplit(as.character(d$V1), split = ",")
d1 <- as.data.frame(t(array(unlist(d1), dim = c(length(d1[[1]]), length(d1)))))
colnames(d1) <- c("Unit", "Sex", "Age", "Icd10", "Geo")
colnames(d) <- c("Remove", 2010:1994)
d <- cbind(d1, d)
d$Remove <- NULL
d <- d[2:nrow(d) , ]
d <- melt(d, measure.vars = 6:ncol(d), variable.name = "Year", value.name = "Result")
d$Result <- gsub("[a-z]", "", d$Result)
d$Result[grepl(":", d$Result)] <- NA
d$Result <- as.numeric(d$Result)
d <- dropall(d)
write.csv(d, file = "//cesium/jtue$/_Documents/MortInEurope.csv", row.names = FALSE)

References